Do you have the VW charcoal canister setup? I tried hooking up one of the vacuum lines to the top throttle body vacuum with a 'tee' on my 02 2.5L. I had a significant (not occasional) rough idle and stalling, when coming to a stop, although it was fine with open throttle. I switched to a Subaru canister. Maybe something wrong with your VW charcoal canister setup if you are using it.
